New Cobra Commander 2 Parallel universe
by scouttroop
Summary: This is a sequel to New Cobra Commander but the story takes place in a parallel universe were Cobra commander isn't finish with his vengeance yet. NarutoXShizuka Black lagoon crossover included.
1. Prologue

**Prologue**

**Hey my fellow readers this new story is a sequel to New Cobra Commander but takes place in a parallel universe. Black lagoon crossover included.**

**Disclaimers: I don't own GI JOE, Naruto or Black lagoon. **

Konohagakure 2, prime universe

"Oh hello there my name is Ray Takashi, I'm a cobra neo viper serving Cobra and if you know me I'm the one who wrote that journal about after the war ended. Where I'm residing is the new Konoha, the Hokage is Hashirama Senju who was resurrected by Cobra commander, his true identity is Naruto Uzumaki Namikaze. He's at Nadeshiko village with his wife Shizuka having a happy family. Oh and what I was going to say is what if there was a parallel universe where Cobra commander manage to kill the people he hates but he isn't finish yet with his vengeance. In this prime universe where I am, peace is settled here, but in a parallel universe peace hasn't settle there yet."

Parallel universe

The elemental nations are still at war against the new faction Cobra. Their ruthless leader know as Cobra commander and his wife Shizuka have been capture by Konoha and place in a maximum security prison in Sunagakure, but the cobra operatives Storm shadow, Zartan, Baroness, Firefly, Destro, Sora and the resurrected Mikoto Uchiha remain at large. Before his and Shizuka's capture he manage to kill Orochimaru, Kabuto, the Akatsuki except for Itachi and Konan, he also killed the people he hates, Danzo Shimura, the shinobi elders, the civilian council and Sasuke Uchiha, but he isn't finish with his vengeance. The entire nations remain on alert for Cobra commander's final goal.

Destruction of Konohagakure

"I think we found them Storm shadow."

"Good Firefly let's get going", Storm shadow said.

"It's going to be great to be back at the elemental nations", Firefly said as he brings his wheel blaster bike into the black dragon VTOL with Storm shadow.

**That's the end of the prologue. The Cobra infantry and vehicles are the same but they will get warships. The people who were resurrected from the last story are not resurrected yet and Kushina is the only one alive since this story takes place in a parallel universe. Cobra commander's identity is not revealed yet in the parallel universe. Please review**

**Next: Prison busted**


	2. Prison busted

**Prison busted**

**Hey my fellow readers here's the next chapter were Cobra commander and Shizuka gets freed.**

**Disclaimers: I own nothing**

Sunagakure maximum security prison

Inside is Cobra commander, Shizuka and now Storm shadow inside water tubes and wearing a white suit (Same white suit in retaliation). Earlier Storm shadow allows himself to be capture and imprisoned while Firefly distract the Suna anbu outside. The trio are guarded my Suna ninjas and Matsuri was in charge of them.

"Welcome to hell Storm shadow", Matsuri said to Storm shadow thinking she can scare him inside the tube.

Outside Firefly stops his wheel blaster bike fitted with MP7 submachine guns. He sends out robot firefly drones to distract the Suna anbu guards. Back inside Storm shadow sees the robot fireflies from a security camera and it's now or never, he pretends that his heart stops beating which made the Suna ninjas comes to his aid. As a Suna medic ninja tries to pull him out of the tube Storm shadow awakens and pulls him in drowning him.

"Oh no kill him!" Matsuri said after realizing Storm shadow has tricked them.

Suna ninja's shoots kunai knifes at him, as the tube shatters Storm shadow throws hidden shuriken at 2 Suna ninjas killing them both, he then kills the last one by snapping his neck. Back outside the robot fireflies that lands on the guards detonates killing them all. Inside again Storm shadow retrieves his katana swords while Matsuri hides from him. He then hides in while Suna ninjas enter the room and sweeps the area.

**Cobra lighting strike"**, Storm shadow uses his technique and delivers a swift and devastating slash to those Suna ninjas killing them all.

"Welcome hell", Storm shadow said to Matsuri making an evil smile on his face.

Matsuri then electrocutes him using the heart pumpers on the water he is standing on and runs away from the room. Outside Firefly drives his bike and fires the MP7 submachine guns at the gate then fires missiles then turns the parts of his bike into missiles destroying the gate giving him an entrance. Firefly Para shoots and land safely to the ground after his bike turn into missiles, as walks into the prison he pulls his duel FNX 45 pistols to shoot anyone that stands in his way. Back inside Storm shadow pulls out Cobra commander's Stealth hunter 629 revolver and frees him. Cobra commander then puts his mask from the white suit back on and gets up and walks up to Storm shadow.

"Storm shadow never adapt", he said to him.

"Cobra commander", Storm shadow said then hands Cobra commander's revolver back to him, he then turns to Shizuka who is still inside the tubes.

"Shizuka, we are going home", Cobra commander said as he shoots the tube freeing her and she lands in his arms.

"Free at last Naruto", Shizuka said in his arms.

Matsuri is trying to open the gate so she can get away from the prison. Next thing the gate in front of her opens and 3 metal balls roll pass her. They detonate and wounded her as she falls to the floor.

"I see you arrange transportation", Cobra commander said as he, Shizuka and Storm shadow walk out the room and sees Firefly at the entrance.

"Making things go boom by 9am. Most people do all day", Firefly said removing his mask.

"Firefly good to see you old friend", Cobra commander greeted him.

"Sir, I busted out 8 prisoners, but I only broke into 1, no one will know that you and Shizuka are not here", Firefly said to them.

A wounded Matsuri throws a kunai at flammable tube next to the 4 of them but they manage to avoid it. Cobra commander shoots Matsuri in the stomach as they get out the prison. Storm shadow has his back badly burn and Firefly helps him to the transportation.

"We get him a medic when we get back", Cobra commander said.

Outside Yugao Uzuki watches them with binoculars, she then pulls out a beretta inox but too late to catch up with them as the black dragon VTOL carrying them flies away.

"I guess the war won't be over soon with Cobra commander and Shizuka back in action", Yugao said as she goes in the prison to check for survivors.

Roanapur a land populated with criminals and a new Cobra command is built but the criminals there don't know their existence yet. When Cobra commander and Shizuka were capture Cobra and its followers abandon their old Cobra command in the snow country, they also destroyed the nanomites not to let it fall to enemy hands but kept the Zeus cannon to use since it's in space. Their plasma guns are also destroyed and replace by bullet weapons this time. Cobra also created their own navy by using the aircraft carrier used by the sky country now refitted into a Nimitz-class aircraft carrier for night ravens, cobra rattlers, sand serpents, cobra gunships, black dragon VTOL and crimson hydras. They also have battleships, battle cruiser and amphibious assault ship.

Cobra command Roanapur

Cobra troopers open the double doors so Cobra commander, Shizuka and Firefly could come in.

"Good to have you back sir", Cobra trooper said.

"Isn't she a beauty?" Firefly asks him about the second Zeus cannon.

"Soon the elemental nation will cower in the face of the second Zeus", Cobra commander said while Shizuka has her arms wrap around his right arm.

"All we been missing is our commander and his wife. It's good to have you back boss and you too Shizuka", Firefly said to them as Cobra commander nods and Shizuka wink at him.

"Welcome back Cobra commander and Shizuka", Zartan said walking up to them.

"How's everyone been Zartan?" Cobra commander asked him.

"Oh nothing much Cobra commander they just been missing you and Shizuka very much", Zartan explains during Cobra commander and Shizuka absents.

"Well I and Shizuka are back now. In 48 hours the second Zeus will launch", Cobra commander said starring at the second Zeus.

"Just one wrinkle, Yugao Uzuki saw you and Shizuka escape, she will warn everyone about this", Zartan said to Cobra commander.

"Can trust you with nothing", Cobra commander growled at him.

"She will slip up and when she do, me or Storm shadow will hump her on the ground", Firefly said to Cobra commander while Shizuka calms him down.

"Hooah, in the meantime let's play are part in Roanapur", Cobra commander said smirking under his helmet.

**Cobra commander outfit is the same in Retaliation. Yugao Uzuki's role like last time is Snake eyes. Firefly and Storm shadow will have a strong friendship with each other in the parallel universe. I hope you enjoyed it and please review.**

**Next: Viper commado strikes Soviets**


	3. Viper commando strikes soviets

**Viper commando strikes soviets**

**Hey guys here's the next chapter were Viper commandos attacks Balalaika's people. I hope you enjoy it.**

**Disclaimers: I own nothing**

When Cobra commander and Shizuka were freed from their prison by Storm shadow and Firefly they decided to play their role in Roanapur while the second Zeus cannon is being build and ready to launch.

Elsewhere

A team of ex-spetsnaz who are loyal to Balalaika are on their way back after picking some supplies of special weapons like a minigun and new AK assault rifles. But their home coming is about to be interrupted by the new faction in Roanapur known as Cobra.

"Hey comrade how long till we get there", one said to the other who's driving.

"We are half way there comrade private", he said to him.

Above them a cobra gunship flies and attacks them with its pulse cannon which destroyed one of the trucks. The cobra gunship comes for another pass ex-spetsnaz soldiers open fires at it with their AK-47, AK-74 and G3 assault rifles but the gunship is not even being scratch at all. Then they fire a stinger missile at the gunship but get blown out of the air due the cobra gunship's minigun. The cobra gunship fires its pulse cannon again hitting another truck making it flip over 3 times.

"Its landing, hurry let's help a comrades from the truck then we will fight", an ex-spetsnaz soldier said as they help their comrades from the truck that flip over.

Back at the cobra gunship squads of Viper commandos armed with ARX-160 assault rifles and desert eagle pistols exits the gunship heads off to fight and kill all the ex-spetsnaz soldiers. Along with them is baroness and she is armed duel Beretta 87 FS target.

Flashback

"Remember what Cobra commander told us we attack Balalaika's men. Leave no survivors in the area", Baroness said to the squad while loading her Beretta 87 FS target.

"Yes maim", they all said to her.

End of flashback

Balalaika's men fire an RPG at the Viper commandos, they fire their assault rifles at them but the Viper commandos have a strong armor they never seen before (like in rise of cobra). They even throw grenades at them but they are untouched by the explosions. Viper commandos open fire at them killing a lot of them and some of them have to take cover but are also killed by the Viper commandos who are throwing grenades. Baroness kills 2 guys trying to get way.

"Nobody runs away from the fight", she said smirking.

The last ex-spetsnaz armed with a MAG-7 pump action shotgun attempts to get away but is spotted by a lone Viper commando. He fires his shotgun making the Viper commando fall in his back but gets up. He fires again but still gets back up. Viper commando shoots him in the foot making the ex-spetsnaz drop his shotgun. He tries to crawl to his shotgun but the Viper commando steps on it preventing him from picking it up.

"Bye-bye", Viper commando said blowing his head off with ARX-160 assault rifle.

After killing them all Baroness orders the squad to destroy the remaining trucks including the bodys with a lot of C4s. For the weapons they just take the minigun and destroyed the rest. After all that they head back to gunship and head back to Cobra command.

"I wonder what's everybody else doing", Baroness said to herself

Meanwhile in Elemental nation

Yugao already warn everybody about Cobra commander and Shizuka's return to action but the problem is they have no idea where they went. Yugao is starring at a blue print of an aircraft she might get some people to build so she can find Cobra commander and his military. She still has the nanomites inside her but it's giving her knowledge about Cobra's bullet weapons, this how she gets to use her Beretta Inox. She calls the aircraft Ghost hawk (retaliation).

**Well that's the end of this chapter, I know Viper commandos and Neo vipers used pulse rifles but since I said their advance weapons are gone they now use bullet weapons.**

**Next: Neo viper strikes triads**


	4. Neo viper strikes triads

**Neo viper strikes triads**

**Ok guys here's the next wave on the chapter were the Neo vipers will attack Chang's people.**

**Disclaimers: I own nothing**

The Viper commandos and Baroness did their part in Roanapur. The Neo vipers will do their part now by attacking Chang's triads.

Triad building

Chang is busy smoking inside his building he heard the news from Balalaika, the convoy was attack which was caused by Cobra but they don't know about them because they are new to Roanapur. Outside hummers with Neo vipers armed XM8 assault rifles and M9 pistols are going attack Chang and his people.

"Our objective is to shoot and kill the triads except for mister Chang don't kill him, is that understood", the Neo viper leader said to his team.

"Yes sir", the rest said.

They park their hummers in dark corners so no one will notice them and they moved in quietly. They put silencers on their M9 pistols and kills the guards quietly also catches them before they hit the ground and drag them away before anyone would notice.

"Squad one move in", Neo viper leader order the first squad.

Chang notice them through security camera which the Neo vipers shoot. Chang and his bodyguards draw guns out aim it at the door were they will be coming in. It will take them a while because the Neo vipers will have to use the elevator to get to Chang.

"I just hope the others get this message", Chang said sending a message to the others while they wait for the Neo vipers.

An hour later the door burst open and 2 Neo vipers enter the room then Chang and his bodyguards open fire at them but that armor is very strong, not a single bullet getting threw it.

"Secure your area", the Neo viper leader said through the radio.

"Were on it", the Neo viper said as he and his teammate open fire killing Chang's bodyguards.

"Clear", he said before knocking Chang out then drags him out of the building.

While they were trying to get to Chang the other squad members kill all of the triads leaving the building empty.

"Ok leave mister Chang here at the entrance he can tell the others about this", the Neo viper leader said as they make their way back to the hummers.

"I just wonder what's the next mission that everybody else in Cobra will be doing", I Neo viper said to himself as they drive their hummers back to Cobra command.

Cobra command

Cobra commander sits in his new command chair until he gets a call. He opens a channel to see an old man is calling him.

"Hello Cobra commander I'm Sir Alfred and I have a job that you might be interested in", the old man said to him.

"And that is Sir Alfred?" Cobra commander said.

"I want you to retrieve a painting. It's called the twelve knights led by Brunhilda, it's found in a sunken Nazi submarine", Sir Alfred explain to him as Cobra commander gets an image of the painting.

"Very well then my forces will retrieve it as long you are paying me", Cobra commander said.

"I will pay you but you better hurry because I also hired the Lagoon Company and Neo-Nazi for the job so they are after the same thing", Sir Alfred warns Cobra commander about the 2 competitors for the job.

"Will see about that", Cobra commander said turning off the channel.

'I will be accompany my forces in this mission', Cobra commander thought to himself as he leaves his command chair.

**That's all for this chapter. Please review.**

**Next: The painting**


End file.
